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Datasets:
nicolynnvila
/
splicing_epistasis_okgp_tcga_nondriver_recurrent

Tasks:
Tabular Classification
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Modalities:
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Size:
10K - 100K
Tags:
genomics
splicing
epistasis
1000-genomes
tcga
non-driver
Libraries:
Datasets
pandas
Polars
License:
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epistasis_id
stringlengths
35
51
arm
stringclasses
2 values
gene
stringclasses
611 values
chrom
int64
1
22
mut1
stringlengths
17
25
mut2
stringlengths
17
25
distance
int64
1
100
n_mut1
int64
3
254
n_mut2
int64
3
254
n_both
int64
0
241
LENG8:19:54458749:C:G|LENG8:19:54458824:C:T
observed
LENG8
19
LENG8:19:54458749:C:G
LENG8:19:54458824:C:T
75
33
60
3
ZNF888:19:52922212:T:C|ZNF888:19:52922274:G:C
observed
ZNF888
19
ZNF888:19:52922212:T:C
ZNF888:19:52922274:G:C
62
182
89
4
XAB2:19:7626280:G:A|XAB2:19:7626357:C:T
observed
XAB2
19
XAB2:19:7626280:G:A
XAB2:19:7626357:C:T
77
6
182
1
XAB2:19:7626293:G:C|XAB2:19:7626357:C:T
observed
XAB2
19
XAB2:19:7626293:G:C
XAB2:19:7626357:C:T
64
35
182
1
GLYATL1:11:59043169:T:C|GLYATL1:11:59043202:A:C
observed
GLYATL1
11
GLYATL1:11:59043169:T:C
GLYATL1:11:59043202:A:C
33
50
53
15
HNRNPCL2:1:13116774:A:C|HNRNPCL2:1:13116819:C:T
observed
HNRNPCL2
1
HNRNPCL2:1:13116774:A:C
HNRNPCL2:1:13116819:C:T
45
215
4
2
SMARCC2:12:56184898:T:C|SMARCC2:12:56184974:G:C
observed
SMARCC2
12
SMARCC2:12:56184898:T:C
SMARCC2:12:56184974:G:C
76
169
14
2
SCAMP3:1:155258220:C:T|SCAMP3:1:155258315:G:A
observed
SCAMP3
1
SCAMP3:1:155258220:C:T
SCAMP3:1:155258315:G:A
95
4
156
1
HRC:19:49154252:A:T|HRC:19:49154338:A:G
observed
HRC
19
HRC:19:49154252:A:T
HRC:19:49154338:A:G
86
246
20
18
CLVS1:8:61108451:G:A|CLVS1:8:61108515:T:C
observed
CLVS1
8
CLVS1:8:61108451:G:A
CLVS1:8:61108515:T:C
64
49
31
2
APOBEC3F:22:39053997:G:A|APOBEC3F:22:39054082:G:C
observed
APOBEC3F
22
APOBEC3F:22:39053997:G:A
APOBEC3F:22:39054082:G:C
85
27
51
1
SELP:1:169598244:A:G|SELP:1:169598275:C:T
observed
SELP
1
SELP:1:169598244:A:G
SELP:1:169598275:C:T
31
19
187
2
PPP1R12B:1:202525213:C:G|PPP1R12B:1:202525224:C:T
observed
PPP1R12B
1
PPP1R12B:1:202525213:C:G
PPP1R12B:1:202525224:C:T
11
8
34
1
OSBP2:22:30737480:A:G|OSBP2:22:30737500:T:A
observed
OSBP2
22
OSBP2:22:30737480:A:G
OSBP2:22:30737500:T:A
20
69
29
1
CEACAM5:19:41727336:T:G|CEACAM5:19:41727416:G:A
observed
CEACAM5
19
CEACAM5:19:41727336:T:G
CEACAM5:19:41727416:G:A
80
4
4
4
CLTB:5:176404799:G:A|CLTB:5:176404818:C:T
observed
CLTB
5
CLTB:5:176404799:G:A
CLTB:5:176404818:C:T
19
16
9
1
XCL2:1:168541128:G:A|XCL2:1:168541144:T:C
observed
XCL2
1
XCL2:1:168541128:G:A
XCL2:1:168541144:T:C
16
18
27
2
CTTNBP2:7:117816769:A:G|CTTNBP2:7:117816847:T:C
observed
CTTNBP2
7
CTTNBP2:7:117816769:A:G
CTTNBP2:7:117816847:T:C
78
6
73
3
CD4:12:6798480:C:T|CD4:12:6798564:T:A
observed
CD4
12
CD4:12:6798480:C:T
CD4:12:6798564:T:A
84
31
38
1
CYP2B6:19:41017565:G:A|CYP2B6:19:41017661:A:C
observed
CYP2B6
19
CYP2B6:19:41017565:G:A
CYP2B6:19:41017661:A:C
96
11
11
11
ACSM2B:16:20541444:G:A|ACSM2B:16:20541470:C:A
observed
ACSM2B
16
ACSM2B:16:20541444:G:A
ACSM2B:16:20541470:C:A
26
7
122
1
NLRP1:17:5584433:G:A|NLRP1:17:5584472:C:G
observed
NLRP1
17
NLRP1:17:5584433:G:A
NLRP1:17:5584472:C:G
39
85
13
1
TLR1:4:38823270:G:C|TLR1:4:38823300:T:G
observed
TLR1
4
TLR1:4:38823270:G:C
TLR1:4:38823300:T:G
30
124
21
3
BTN2A1:6:26471188:G:A|BTN2A1:6:26471243:A:G
observed
BTN2A1
6
BTN2A1:6:26471188:G:A
BTN2A1:6:26471243:A:G
55
81
114
5
GABRR2:6:89293348:A:T|GABRR2:6:89293380:G:A
observed
GABRR2
6
GABRR2:6:89293348:A:T
GABRR2:6:89293380:G:A
32
36
21
1
DISC1:1:231762217:T:C|DISC1:1:231762293:C:T
observed
DISC1
1
DISC1:1:231762217:T:C
DISC1:1:231762293:C:T
76
234
22
3
CENPC:4:67490855:T:A|CENPC:4:67490867:T:A
observed
CENPC
4
CENPC:4:67490855:T:A
CENPC:4:67490867:T:A
12
18
118
1
ZMYM4:1:35391796:A:T|ZMYM4:1:35391798:T:C
observed
ZMYM4
1
ZMYM4:1:35391796:A:T
ZMYM4:1:35391798:T:C
2
21
21
21
TUBGCP4:15:43370961:G:C|TUBGCP4:15:43371012:A:G
observed
TUBGCP4
15
TUBGCP4:15:43370961:G:C
TUBGCP4:15:43371012:A:G
51
70
22
2
CYP4F12:19:15680341:G:A|CYP4F12:19:15680430:C:T
observed
CYP4F12
19
CYP4F12:19:15680341:G:A
CYP4F12:19:15680430:C:T
89
102
3
1
ZMYM4:1:35391797:C:A|ZMYM4:1:35391798:T:C
observed
ZMYM4
1
ZMYM4:1:35391797:C:A
ZMYM4:1:35391798:T:C
1
21
21
21
MCCC1:3:183095553:T:A|MCCC1:3:183095573:T:C
observed
MCCC1
3
MCCC1:3:183095553:T:A
MCCC1:3:183095573:T:C
20
14
45
1
PFKFB2:1:207080932:T:G|PFKFB2:1:207080969:G:A
observed
PFKFB2
1
PFKFB2:1:207080932:T:G
PFKFB2:1:207080969:G:A
37
229
53
53
CCDC152:5:42769190:G:T|CCDC152:5:42769226:C:T
observed
CCDC152
5
CCDC152:5:42769190:G:T
CCDC152:5:42769226:C:T
36
13
50
1
SEZ6L:22:26343396:T:A|SEZ6L:22:26343416:A:T
observed
SEZ6L
22
SEZ6L:22:26343396:T:A
SEZ6L:22:26343416:A:T
20
11
114
2
TACC1:8:38806477:A:T|TACC1:8:38806488:A:G
observed
TACC1
8
TACC1:8:38806477:A:T
TACC1:8:38806488:A:G
11
32
152
9
EPSTI1:13:42931862:T:G|EPSTI1:13:42931905:A:C
observed
EPSTI1
13
EPSTI1:13:42931862:T:G
EPSTI1:13:42931905:A:C
43
5
8
5
UBE2Q1:1:154555223:T:C|UBE2Q1:1:154555227:T:C
observed
UBE2Q1
1
UBE2Q1:1:154555223:T:C
UBE2Q1:1:154555227:T:C
4
3
3
3
MOV10:1:112678429:C:T|MOV10:1:112678510:A:G
observed
MOV10
1
MOV10:1:112678429:C:T
MOV10:1:112678510:A:G
81
80
9
1
CNTN3:3:74436402:C:A|CNTN3:3:74436418:A:G
observed
CNTN3
3
CNTN3:3:74436402:C:A
CNTN3:3:74436418:A:G
16
80
125
1
CRISP1:6:49836342:T:A|CRISP1:6:49836346:T:A
observed
CRISP1
6
CRISP1:6:49836342:T:A
CRISP1:6:49836346:T:A
4
41
252
1
ATN1:12:6925187:G:A|ATN1:12:6925190:C:T
observed
ATN1
12
ATN1:12:6925187:G:A
ATN1:12:6925190:C:T
3
4
89
1
NUCKS1:1:205742497:T:A|NUCKS1:1:205742502:C:T
observed
NUCKS1
1
NUCKS1:1:205742497:T:A
NUCKS1:1:205742502:C:T
5
248
15
1
ZNF569:19:37433245:C:G|ZNF569:19:37433254:G:A
observed
ZNF569
19
ZNF569:19:37433245:C:G
ZNF569:19:37433254:G:A
9
11
40
2
IFNA10:9:21206570:C:A|IFNA10:9:21206579:T:A
observed
IFNA10
9
IFNA10:9:21206570:C:A
IFNA10:9:21206579:T:A
9
79
7
1
ABCA5:17:69281559:T:A|ABCA5:17:69281591:A:C
observed
ABCA5
17
ABCA5:17:69281559:T:A
ABCA5:17:69281591:A:C
32
3
123
1
PFKFB2:1:207061129:C:A|PFKFB2:1:207061143:T:A
observed
PFKFB2
1
PFKFB2:1:207061129:C:A
PFKFB2:1:207061143:T:A
14
50
33
2
BCAS1:20:54016279:C:T|BCAS1:20:54016280:A:G
observed
BCAS1
20
BCAS1:20:54016279:C:T
BCAS1:20:54016280:A:G
1
17
17
17
MYO1B:2:191299799:A:G|MYO1B:2:191299840:A:T
observed
MYO1B
2
MYO1B:2:191299799:A:G
MYO1B:2:191299840:A:T
41
101
3
3
SMCHD1:18:2708818:G:T|SMCHD1:18:2708905:T:A
observed
SMCHD1
18
SMCHD1:18:2708818:G:T
SMCHD1:18:2708905:T:A
87
9
57
2
RIMBP2:12:130580957:G:T|RIMBP2:12:130580960:T:C
observed
RIMBP2
12
RIMBP2:12:130580957:G:T
RIMBP2:12:130580960:T:C
3
128
25
1
SAP130:2:127990519:T:C|SAP130:2:127990583:C:T
observed
SAP130
2
SAP130:2:127990519:T:C
SAP130:2:127990583:C:T
64
73
27
1
EPS8:12:15803678:T:C|EPS8:12:15803747:G:A
observed
EPS8
12
EPS8:12:15803678:T:C
EPS8:12:15803747:G:A
69
173
14
1
ATN1:12:6925153:A:T|ATN1:12:6925190:C:T
observed
ATN1
12
ATN1:12:6925153:A:T
ATN1:12:6925190:C:T
37
174
89
17
ZNF880:19:52371667:C:T|ZNF880:19:52371757:C:T
observed
ZNF880
19
ZNF880:19:52371667:C:T
ZNF880:19:52371757:C:T
90
152
31
2
RBM6:3:50006780:A:C|RBM6:3:50006833:T:C
observed
RBM6
3
RBM6:3:50006780:A:C
RBM6:3:50006833:T:C
53
191
40
5
ZNF594:17:5190283:G:A|ZNF594:17:5190376:A:G
observed
ZNF594
17
ZNF594:17:5190283:G:A
ZNF594:17:5190376:A:G
93
98
41
1
SRRT:7:100882020:A:C|SRRT:7:100882045:C:T
observed
SRRT
7
SRRT:7:100882020:A:C
SRRT:7:100882045:C:T
25
45
5
5
SEZ6L:22:26328501:C:G|SEZ6L:22:26328542:G:A
observed
SEZ6L
22
SEZ6L:22:26328501:C:G
SEZ6L:22:26328542:G:A
41
9
8
1
CDHR5:11:622136:G:A|CDHR5:11:622181:C:T
observed
CDHR5
11
CDHR5:11:622136:G:A
CDHR5:11:622181:C:T
45
194
3
1
TMED6:16:69351478:G:A|TMED6:16:69351523:G:A
observed
TMED6
16
TMED6:16:69351478:G:A
TMED6:16:69351523:G:A
45
3
64
1
ZFP64:20:52053398:C:A|ZFP64:20:52053409:A:T
observed
ZFP64
20
ZFP64:20:52053398:C:A
ZFP64:20:52053409:A:T
11
35
152
1
SUN1:7:828333:G:A|SUN1:7:828364:T:C
observed
SUN1
7
SUN1:7:828333:G:A
SUN1:7:828364:T:C
31
24
4
3
ZNF761:19:53450043:G:A|ZNF761:19:53450082:A:G
observed
ZNF761
19
ZNF761:19:53450043:G:A
ZNF761:19:53450082:A:G
39
52
44
2
CDS1:4:84609477:G:A|CDS1:4:84609480:G:T
observed
CDS1
4
CDS1:4:84609477:G:A
CDS1:4:84609480:G:T
3
12
152
1
PPP1R12B:1:202439012:C:T|PPP1R12B:1:202439082:A:G
observed
PPP1R12B
1
PPP1R12B:1:202439012:C:T
PPP1R12B:1:202439082:A:G
70
6
5
5
RARG:12:53221693:C:T|RARG:12:53221786:C:A
observed
RARG
12
RARG:12:53221693:C:T
RARG:12:53221786:C:A
93
65
6
1
EPSTI1:13:42909096:A:T|EPSTI1:13:42909102:T:C
observed
EPSTI1
13
EPSTI1:13:42909096:A:T
EPSTI1:13:42909102:T:C
6
42
173
15
WNT8A:5:138086351:G:T|WNT8A:5:138086364:T:A
observed
WNT8A
5
WNT8A:5:138086351:G:T
WNT8A:5:138086364:T:A
13
3
3
3
IFNA10:9:21206570:C:A|IFNA10:9:21206593:C:T
observed
IFNA10
9
IFNA10:9:21206570:C:A
IFNA10:9:21206593:C:T
23
79
13
1
SEZ6L:22:26327586:G:A|SEZ6L:22:26327636:C:T
observed
SEZ6L
22
SEZ6L:22:26327586:G:A
SEZ6L:22:26327636:C:T
50
3
3
3
NEIL3:4:177324637:T:C|NEIL3:4:177324672:A:G
observed
NEIL3
4
NEIL3:4:177324637:T:C
NEIL3:4:177324672:A:G
35
4
16
4
CD96:3:111634558:G:A|CD96:3:111634601:T:C
observed
CD96
3
CD96:3:111634558:G:A
CD96:3:111634601:T:C
43
29
45
1
ITCH:20:34467173:G:A|ITCH:20:34467196:C:T
observed
ITCH
20
ITCH:20:34467173:G:A
ITCH:20:34467196:C:T
23
28
60
28
PFN2:3:149969050:T:C|PFN2:3:149969064:A:G
observed
PFN2
3
PFN2:3:149969050:T:C
PFN2:3:149969064:A:G
14
42
63
1
SMYD1:2:88092117:G:C|SMYD1:2:88092214:C:A
observed
SMYD1
2
SMYD1:2:88092117:G:C
SMYD1:2:88092214:C:A
97
7
51
1
HNRNPM:19:8478955:C:T|HNRNPM:19:8479043:T:C
observed
HNRNPM
19
HNRNPM:19:8478955:C:T
HNRNPM:19:8479043:T:C
88
217
3
1
SV2C:5:76088801:A:T|SV2C:5:76088841:A:C
observed
SV2C
5
SV2C:5:76088801:A:T
SV2C:5:76088841:A:C
40
121
6
6
CERCAM:9:128426362:C:T|CERCAM:9:128426447:C:T
observed
CERCAM
9
CERCAM:9:128426362:C:T
CERCAM:9:128426447:C:T
85
26
35
1
LENG8:19:54456556:G:A|LENG8:19:54456567:G:A
observed
LENG8
19
LENG8:19:54456556:G:A
LENG8:19:54456567:G:A
11
32
60
3
EPB41L1:20:36151470:A:T|EPB41L1:20:36151566:T:G
observed
EPB41L1
20
EPB41L1:20:36151470:A:T
EPB41L1:20:36151566:T:G
96
5
226
5
CD300A:17:74482720:T:C|CD300A:17:74482811:A:G
observed
CD300A
17
CD300A:17:74482720:T:C
CD300A:17:74482811:A:G
91
10
16
1
CHD1L:1:147289626:C:T|CHD1L:1:147289710:A:G
observed
CHD1L
1
CHD1L:1:147289626:C:T
CHD1L:1:147289710:A:G
84
3
18
1
ZNF569:19:37428736:G:A|ZNF569:19:37428766:C:T
observed
ZNF569
19
ZNF569:19:37428736:G:A
ZNF569:19:37428766:C:T
30
71
33
4
OR1M1:19:9091575:C:T|OR1M1:19:9091583:T:C
observed
OR1M1
19
OR1M1:19:9091575:C:T
OR1M1:19:9091583:T:C
8
25
9
1
ZRANB3:2:135455784:C:T|ZRANB3:2:135455807:G:A
observed
ZRANB3
2
ZRANB3:2:135455784:C:T
ZRANB3:2:135455807:G:A
23
27
60
1
ZNF778:16:89218190:C:T|ZNF778:16:89218192:G:T
observed
ZNF778
16
ZNF778:16:89218190:C:T
ZNF778:16:89218192:G:T
2
15
15
15
CEP164:11:117348988:T:G|CEP164:11:117348997:A:T
observed
CEP164
11
CEP164:11:117348988:T:G
CEP164:11:117348997:A:T
9
3
3
3
TLR1:4:38801907:T:C|TLR1:4:38801983:G:A
observed
TLR1
4
TLR1:4:38801907:T:C
TLR1:4:38801983:G:A
76
130
76
5
CCR8:3:39331426:C:G|CCR8:3:39331436:C:T
observed
CCR8
3
CCR8:3:39331426:C:G
CCR8:3:39331436:C:T
10
19
128
1
ATP1A2:1:160139818:C:G|ATP1A2:1:160139862:T:C
observed
ATP1A2
1
ATP1A2:1:160139818:C:G
ATP1A2:1:160139862:T:C
44
10
4
1
CLVS1:8:61059433:A:G|CLVS1:8:61059501:C:T
observed
CLVS1
8
CLVS1:8:61059433:A:G
CLVS1:8:61059501:C:T
68
12
57
1
ITIH5:10:7608837:A:C|ITIH5:10:7608937:A:T
observed
ITIH5
10
ITIH5:10:7608837:A:C
ITIH5:10:7608937:A:T
100
76
75
5
ATP2B4:1:203641803:A:G|ATP2B4:1:203641844:C:T
observed
ATP2B4
1
ATP2B4:1:203641803:A:G
ATP2B4:1:203641844:C:T
41
5
19
1
CYP2B6:19:41017565:G:A|CYP2B6:19:41017571:G:A
observed
CYP2B6
19
CYP2B6:19:41017565:G:A
CYP2B6:19:41017571:G:A
6
11
11
11
RPN2:20:37216564:C:T|RPN2:20:37216586:C:G
observed
RPN2
20
RPN2:20:37216564:C:T
RPN2:20:37216586:C:G
22
60
4
1
SLC7A2:8:17552769:C:G|SLC7A2:8:17552807:G:A
observed
SLC7A2
8
SLC7A2:8:17552769:C:G
SLC7A2:8:17552807:G:A
38
6
118
1
MYO1G:7:44968802:T:C|MYO1G:7:44968893:A:C
observed
MYO1G
7
MYO1G:7:44968802:T:C
MYO1G:7:44968893:A:C
91
6
43
1
MCCC1:3:183037865:A:T|MCCC1:3:183037957:C:T
observed
MCCC1
3
MCCC1:3:183037865:A:T
MCCC1:3:183037957:C:T
92
24
31
1
ZNF880:19:52370845:G:A|ZNF880:19:52370930:G:A
observed
ZNF880
19
ZNF880:19:52370845:G:A
ZNF880:19:52370930:G:A
85
3
151
2
End of preview. Expand in Data Studio

Splicing epistasis — Non-driver+TCGA-recurrent panel (Panel B)

94,984 cis-double SNV pairs (47,492 observed + 47,492 unobserved-matched) in 1000 Genomes across 663 genes that satisfy:

  • NOT in OncoKB cancerGeneList.tsv, AND
  • carry ≥2 TCGA-clean double-mutation pairs each with ≥5 carriers (per tcga_de_novo_pairs_clean.csv from the original paper-2 code dump)

Built as the non-driver arm of a three-panel strict test. These are genes that show recurrent doublet events in TCGA cancers but are not classified as cancer drivers.

Methodology

Same as paper §2 ¶1-5:

  • ≤100 nt intra-gene window
  • ≥3 1KG carriers per constituent
  • TopLD r² ≥ 0.2 dropped
  • Greedy 1:1 matched arms keyed on gene + log-rarity bin + distance ±2 nt
  • seed=42

Files

  • inputs.parquet — 94,984 matched-arm pairs
  • gene_panel.txt — the 663-gene list
  • stats.json — enumeration / matching counts
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